protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup Member List

This is the complete list of members for protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup, including all inherited members.

added_cutpoint_closed_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
alignment_res_string_list_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
allow_chain_boundary_jump_partner_right_at_fixed_BP_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
allow_fixed_res_at_moving_res_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
apply()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	virtual
assert_jump_point_in_fixed_res_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
check_moving_res_in_chain(Size const &start_chain, Size const &end_chain, Size const &num_chains, Size &which_chain_has_moving_res)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
cutpoint_open_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
cuts_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_best_working_alignment()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_chain_boundaries()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_cuts()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_gap_size_and_five_prime_chain_break_res()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_is_prepend_map()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_is_residue_prepend(core::Size const seq_num) const	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_jump_partners()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_partition_definition()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_prepend_internal(core::Size const root_res, InternalWorkingResidueParameter const &internal_params)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_working_alignment(Size const &root_res)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_working_moving_suite()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
figure_out_working_sequence_and_mapping()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
filter_user_alignment_res_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
fixed_res_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
force_fold_tree(core::kinematics::FoldTree const &fold_tree)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
force_fold_tree_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
force_internal_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
force_user_defined_jumps_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
get_previously_closed_cutpoint_from_imported_silent_file() const	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
get_user_input_alignment_res_list(core::Size const root_res)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
input_struct_definition(core::Size const working_seq_num)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
input_tags_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
is_cutpoint_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
job_parameters()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
job_parameters_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
jump_partners_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
jump_point_pair_list_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
moving_res_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
moving_res_list_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
reroot_fold_tree(core::Size const fake_working_moving_suite)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
reroot_fold_tree_simple()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
set_add_virt_res_as_root(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_alignment_res(utility::vector1< std::string > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_allow_chain_boundary_jump_partner_right_at_fixed_BP(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_allow_fixed_res_at_moving_res(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_assert_jump_point_in_fixed_res(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_calc_rms_res(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_cutpoint_closed_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_filter_user_alignment_res(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_fixed_res(utility::vector1< core::Size > const &fixed_res)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_floating_base(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_floating_base_anchor_res(Size const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_force_internal(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_force_north_sugar_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_force_south_sugar_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_force_syn_chi_res_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_force_user_defined_jumps(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_global_sample_res_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_input_tags(utility::vector1< std::string > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_jump_point_pair_list(utility::vector1< std::string > const &jump_point_pairs_string)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_native_alignment_res(utility::vector1< Size > const &native_alignment)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_output_extra_RMSDs(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_protonated_H1_adenosine_list(utility::vector1< core::Size > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_rebuild_bulge_mode(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_sample_both_sugar_base_rotamer(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
set_silent_files_in(utility::vector1< std::string > const &setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_simple_append_map(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_skip_complicated_stuff(bool const setting)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	inline
set_terminal_res(utility::vector1< core::Size > const &terminal_res)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
setup_additional_cutpoint_closed()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
setup_floating_base_jump_to_anchor()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
setup_fold_tree()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
silent_files_in_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
simple_append_map_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
skip_complicated_stuff_	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	private
StepWiseRNA_JobParametersSetup(utility::vector1< core::Size > const &moving_res_list, std::string const &full_sequence, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &input_res2, utility::vector1< core::Size > const &cutpoint_open, Size const &cutpoint_closed)	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup
~StepWiseRNA_JobParametersSetup()	protocols::stepwise::sampling::rna::legacy::StepWiseRNA_JobParametersSetup	virtual